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Yorodumi- PDB-2gl2: Crystal structure of the tetra mutant (T66G,R67G,F68G,Y69G) of ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gl2 | ||||||
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Title | Crystal structure of the tetra mutant (T66G,R67G,F68G,Y69G) of bacterial adhesin FadA | ||||||
Components | adhesion A | ||||||
Keywords | CELL ADHESION / antiparallel helix-loop-helix / FadA Gly4 mutant | ||||||
Function / homology | Adhesion protein FadA / Adhesion protein FadA / Helix Hairpins - #1700 / : / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / : / Adhesion A Function and homology information | ||||||
Biological species | Fusobacterium nucleatum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nithianantham, S. / Xu, M. / Wu, N. / Shoham, M. / Han, Y.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum. Authors: Nithianantham, S. / Xu, M. / Wu, N. / Han, Y.W. / Shoham, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gl2.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gl2.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gl2_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 2gl2_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 2gl2_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 2gl2_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/2gl2 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/2gl2 | HTTPS FTP |
-Related structure data
Related structure data | 2avr S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13329.401 Da / Num. of mol.: 2 / Fragment: residues 19-129 / Mutation: T66G, R67G, F68G, Y69G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Plasmid: pYH1378 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 57117488, UniProt: Q5I6B0*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4.6 Details: Sodium acetate, beta-octyl glucoside, pH 4.6, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2006 / Details: Mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 11518 / Num. obs: 11518 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.062 / Χ2: 1.243 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible obs: 49.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.56 / Num. unique obs: 632 / Χ2: 1.52 / % possible all: 48.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2AVR 2avr Resolution: 2.5→29.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 34.271 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.112 Å2
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Refine analyze | Luzzati coordinate error obs: 0.371 Å / Luzzati sigma a obs: 0.214 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.54 Å /
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Xplor file |
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